Only 5 years passed from CoS to TDH Part 2. It should have had flesh left on it, but all they show are only bones. The chamber is not said to have bugs, creatures or anyone alive within it, so the flesh can't have been eaten.

@SovereignSun You are taking about them as though they aren't magical creatures, but are merely fictional ordinary ones. However, unicorns aren't simply horses that happen to have a horn. Thestrals aren't simply horses with wings. And Basilisks aren't simply big snakes. These animals are magical, which means that the way they interact with nature is innately different from an ordinary animal. And, since decomposition is directly related to the way in which living things interacts with the rest of nature, it's pretty safe to assume that they would do that differently from ordinary animals.
– Misha RMay 7 '18 at 17:21

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@AnthonyGrist Given the lack of evidence - I'd say we have at least one dead basilisk's worth of evidence. But even if we didn't, it would be safe to assume that interacting differently with nature might affect their decomposition. How exactly it might affect their decomposition is a less safe assumption.
– Misha RMay 7 '18 at 17:51

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Well the Chamber of Secrets is literally in a sewer, why would you assume there's no bacteria down there?
– Azor AhaiMay 7 '18 at 21:33

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“The chamber is not said to have bugs, creatures or anyone alive within it, so the flesh can't have been eaten.” — That is a strange assumption. Dead things are eaten by microorganisms. Virtually every surface on Earth is teeming with them. It would be very strange indeed if the sewers (out of all places) in Hogwarts weren’t. Incidentally I’ll disagree here with some other commenters: barring evidence to the contrary, the default assumption should be that magical creatures decay the same way non-magical creatures do. Five years is plenty of time for a carcass to be decay w/ help from rodents
– Konrad RudolphMay 8 '18 at 8:59

4 Answers
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The basilisk’s corpse was never actually seen in the books.

When Ron and Hermione bring Harry the basilisk fangs in the book, the dead body of the basilisk isn’t seen or described in detail. It’s unclear in the book what state of decay the basilisk was in, it’s just said that Ron and Hermione took the fangs from it.

“Harry’s eyes dropped to the objects clutched in Ron and Hermione’s arms: great, curved fangs torn, he now realised, from the skull of a dead Basilisk.” - Harry Potter and the Deathly Hallows, Chapter 31 (The Battle of Hogwarts)

They don’t describe the dead basilisk to Harry, and the reader isn’t “there” when they remove the fangs. In the book, there’s nothing indicating if the dead basilisk was a skeleton or a rotting corpse.

Little is stated about the decaying process of magical creatures.

Basilisks may not be equivalent to “normal” creatures - it’s nowhere near certain that any individual type of magical creature, unless it’s specifically mentioned, would decompose in the same way as “mundane” creatures. Magical creatures do many things mundane creatures cannot - as just one example, the Ashwinder, another type of magical serpent, is created by fire rather than being born in any typical manner, and collapses into dust when it dies.

The Ashwinder lives for only an hour and during that time seeks a dark and secluded spot in which to lay its eggs, after which it will collapse into dust.” - Fantastic Beasts and Where to Find Them

We can’t reasonably presume that a basilisk would decay in the same way as any mundane creature. We also don’t know if the same sort of creatures that would consume mundane animal bodies would be even able to consume the body of a creature like the basilisk - this may be different as well.

Out-of-universe, it could have been done because it looked better on-screen.

To show the dead basilisk on-screen, the filmmakers may have considered it better to show a skeleton rather than a decaying body. This could be for many reasons, for example to create visual impact, or possibly because they considered showing a decaying body to be needlessly gross.

@FezVrasta With that logic there's not a single point for any question here to do with Harry Potter; and as such it's ridiculous to suggest that it's a valid statement at all. Your comment isn't at all a summary of the answer from Miss Bella (well done as usual!); on the contrary she's pointing out how it's not even described in the book but also screen effect as one possible reason. Neither of those have anything to do with 'magic'.
– PryftanMay 8 '18 at 19:31

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FWIW, decaying things do look gross. It's not at all unreasonably to take a little poetic license and make it a skeleton instead of a body, like you said.
– Nic HartleyMay 9 '18 at 7:09

In the books there were the remains of small animals within the tunnel leading to the Chamber itself:

But the tunnel was quiet as the grave, and the first unexpected sound they heard was a loud crunch as Ron stepped on what turned out to be a rat's skull. Harry lowered his wand to look at the floor and saw that it was littered with small animal bones.Harry Potter and the Chamber of Secrets, Chapter Sixteen - The Chamber of Secrets

While this isn't direct evidence of living creatures down there, it seems unlikely that there were none at all. The basilisk didn't appear to have free access to the tunnel leading up to the Chamber, which raises the question of where all of these animal bones came from; the most logical conclusion seems to be that they're the primarily corpses of living animals that happened to die - from whatever cause - within the tunnel.

Small animals can often gain access to places that humans - or a huge basilisk - can't. Hogwarts - and the Chamber of Secrets - were at least a thousand years old, so there were likely gaps sufficient to allow small animals to get in and out of the Chamber itself, and to feed on the corpse of the basilisk.

@AnthonyGrist I figured it ate them elsewhere in the castle (whenever it has access, hibernating and not eating anything when the Chamber is sealed) and then coughed up their bones later, and that there were lots because rats are small and it's big.
– MissMonicaEMay 7 '18 at 17:54

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Huh, interesting! I based that on snakes regurgitating egg shells, and figured it would be too fastidious to litter its home/shrine to Slytherin with gross ole bones.
– MissMonicaEMay 7 '18 at 18:12

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Note that there was also a giant snakeskin in the same area as the bones. While it may not have always had ready access to that area, it clearly did at some time: The light slid over a gigantic snake skin, of a vivid, poisonous green, lying curled and empty across the tunnel floor. The creature that had shed it must have been twenty feet long at least.
– GeobitsMay 7 '18 at 19:25

Only 5 years passed - the basilisk should have had flesh left on it, but all they show are only bones.

Decomposition of dead bodies happens a lot faster than that, even for large animals. It takes about a year until skeletonisation, whether for a pig or for an elephant. I don't think it would be much different for a large snake - and even for a magical snake we should assume that any magical self-protection fails upon its death.

The chamber is not said to have bugs, creatures or anyone alive within it, so the flesh can't have been eaten.

It's not said to have no bugs or living creatures either. It's a large cave, unlikely not to be accessible from the outside. In the books, rats are mentioned explicitly - and even if the basilisk preyed upon them, it doesn't any more after its death.

Even assuming there are no bugs (or larger animals), the microfauna of the basilisk itself is well capable of destroying it from the inside. In the films we can also see large amounts of water in the cave, which might have slowed down decomposition, but it was at least partially exposed to the air. Ron and Hermione get the fangs from a dry skeleton at least.

If you read the linked article about the elephant it specifically mentions that large carnivores are a significant element in the first stages. They would be missing for the Basilisk. Otherwise great answer!
– Angelo FuchsMay 8 '18 at 17:03

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Actually, I would expect water to speed up decomposition. Seals that that get lost and head into the dry valleys of Antarctica don't decompose over hundreds or thousands of years. (The fact it is cold helps preserve them, but it is mostly the fact it is very, very dry.)
– Martin BonnerMay 9 '18 at 7:16

@user76377 I had expected that as well, but it appears exposure to oxygen is what speeds up the process compared to a body underwater. At least regarding the short-term effects (~days), as that's what most sites I found discuss. I don't know about the long run, but intuitively a wet environment should be better for decomposition than a completely dry one, agreed.
– BergiMay 9 '18 at 10:21

It was eaten, just not by other lifeforms, this assumes that Basilisks use a Cytotoxic venom that they have limited immunity to, said immunity being based on a stomach lining like mucus membrane that must be continuously replaced and which separates the toxin from the rest of the Basilisk. As such once the creature is dead it's own venom rapidly leaks out of its venom sacs and spreads through its soft tissue and dissolves it from the inside out. It could decay to a skeletal state in just days.

Is there any evidence from the books or movies to justify these assumptions?
– Anthony GristMay 7 '18 at 17:09

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@AnthonyGrist Only the fact that Basilisk Venom is described as "corrosive" which would generally suggest a Cytotoxin rather than any other class of poison.
– AshMay 7 '18 at 17:13

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Sounds plausible. You should add any quotes that describe - or show - it as corrosive to your answer to support your assumption. Would the fact that the basilisk fangs were still capable of destroying Horcruxes five years later contradict your theory that the basilisk's venom leaked out to aid decomposition?
– Anthony GristMay 7 '18 at 17:19

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Not bad, but there is no reason why the venom should spread all over the basilisk's soft tissues. If you were right, what we would likely see is the total decay of the tissue closest to the venom glands (and possibly the mouth) - but, likely, also a lot of soft tissue untouched by venom that is only partially decayed.
– Misha RMay 7 '18 at 17:30

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@Ash Heh. I would say that capillary action might have more to do with it in that scenario, since it puts less demand on the venom gland structure and decay rate. But even so, judging by the size of the basilisk, you would need a lot of venom to break down all of it. I think the stronger argument is that we don't see the entire body.
– Misha RMay 7 '18 at 17:59